There were 72501 cells passing the quality control in the article, and 11407 of them were sampled from wilms patients. It will be included in this analysis if the cell passed the QC and were from wilms patients.
The first round of annotation followed the pipeline as “clustering –> finding differentially expressed gene –> manual annotation”. As the author instructed, the batch effect between different 10X channels was removed via “harmony”.
The ratio of CD4/CD8 Tcell based on manual annotation is (batch
effect has been removed):
Wilms1: 1.3560606
Wilms2: 0.1666667
Wilms3: 2.5378151
The ratio of CD4/CD8 Tcell based on SingleR annotation is :
Wilms1: 3.7346939
Wilms2: 0.75
Wilms3: 15.5384615
The ratio is calculated as the sum of T regulatory and Th cell divide
by the count of CD8 T cell.
Wilms1: 0.8969072
Wilms2: 4.5
Wilms3: 5.9310345